maqview upper and lower case

[AnamikaDarwin]

Hello,

What is the difference between lower case vs upper case letters are in the maq viewer?

From the maq manual, for the command maq cns2fq it states "bases in lower case are essentially repeats or do not have sufficient coverage; bases in upper case indicate regions where SNPs can be reliably called"

Is this valid for the viewer as well?

Thanks!
Anamika

[swbarnes2]

I'm only familiar with the pile-up, but there, I think that case indicate direction, upper-case is forward, lower-case reverse. It makes sense to keep that in the viewer, so that's probably what it means.

[AnamikaDarwin]

I'm only familiar with the pile-up, but there, I think that case indicate direction, upper-case is forward, lower-case reverse. It makes sense to keep that in the viewer, so that's probably what it means.

swbarnes,

This I am aware of. However, in maqview, on the same read I have a combination of upper and lower case letters.

Thanks!
Anamika

[ruanjue]

In maqview, upper case indicates a higher quality (>= 27), visa verse lower case